The mammalian endoplasmic reticulum (ER) unfolded protein response (UPR), as we know it, consists of a translational arm that modulates protein synthesis in response to ER stress and a transcriptional arm that modulates gene expression. Most of the UPR's targets can be understood in the context of a simple homeostatic ...

Escherichia coli has developed numerous systems to counteract the effects of environmental acidity. One of these systems consists of an inducible lysine decarboxylase (LdcI/ CadA) and a lysine-cadaverine antiporter (CadB). LdcI is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that decarboxylates lysine to produce the polyamine cadaverine and carbon dioxide in a reaction ...

Molecular chaperones provide essential kinetic assistance to protein folding in the cell, binding non-native species via exposed hydrophobic surfaces and generally releasing them through the action of ATP. We have been studying the mechanism of action of the chaperonin ring assembly GroEL, addressing a number of specific questions, including the ...

Many small single-domain proteins undergo cooperative, switch-like folding/unfolding transitions with very low populations of intermediate (i.e., partially folded) conformations. Contrary to widely held expectations, the experimental phenomenon of cooperative, 2-state-like folding is not accounted for by common notions about driving forces for folding. I will highlight how protein chain models ...

While there has been much progress in understanding how proteins fold in vitro (i.e., in infinite dilution), the much more biologically relevant question is: How do proteins fold in the cell, especially in the context of cellular crowding, chaperonins, and other biological machinery of the cell? We have simulated folding ...

Many protein trafficking diseases arise from mutant proteins that are recognized as mutant but are otherwise functional. We developed a trafficking assay and screen for the endoplasmic reticulum retained [DELTA]F508 cystic fibrosis transmembrane conductance regulator (CFTR) protein, and used this in a large scale screen for chemical "correctors". We have ...

Protein folding for export through the exocytic pathway of the eukaryotic cell is sensitive to the local composition of membrane trafficking components, and requires the assistance of multiple chaperones that define the folding buffer of the cell--the chaperome. Different cell types exploit the variable composition of the chaperome to maintain ...

Tailed double-stranded DNA bacteriophages are the most abundant biological entities on earth. The particles of these viruses are composed of more than 1000 individual protein molecules, encoded by more than 20 different genes. Because of the complexity of phage particle structures, highly regulated assembly pathways are required to achieve their ...

Our work suggests that the forces that govern protein folding exert a profound effect in determining how genotypes are translated into phenotypes, and that this has a strong effect on the evolutionary process in diverse organisms. The role of Hsp90 in chaperoning metastable signal transducers places it in a unique ...

The Ras family of small GTPases control diverse signaling pathways through a conserved "switch" mechanism, which is turned on by the binding of GTP and turned off by GTP hydrolysis. Full understanding of GTPase switch functions requires reliable, quantitative assays for nucleotide binding and hydrolysis. Fluorescently labeled guanine nucleotides, such ...

Our lab specializes in measurements that detect and analyze fluorescence fluctuations due to single molecular dynamics. Study of these previously neglected fluctuations can directly resolve short-lived intermediate states and heterogeneities of the elementary biological activities. Because of these unique capabilities, single-molecule techniques are starting to be used more and more ...

Relaxation of the amide [sup.15]N nucleus in nuclear magnetic resonance experiments on peptides is dominated by the dipolar interaction of [sup.15]N with its attached proton. Importantly, relaxation will only occur when the reorientation frequency of the amide bond vector is "tuned" to the Larmor frequency of [sup.15]N. The population of ...

Antifreeze proteins (AFP) are structurally diverse macromolecules that are found in organisms, such as fish, insects, plants, and bacteria, that are exposed to sub-0 temperatures. These intriguing proteins are capable of interacting with ice, resulting in the inhibition of ice-crystal growth, as well as a noncolligative freezing point depression, a ...

Dehydrins are a family of proteins that accumulate in certain plants in the early stages of development, or in response to dehydrating conditions. The presence of a highly conserved, lysine-rich amino acid sequence, called the Kdomain, is observed in all dehydrins. Some members of this family also contain conserved sequences, ...

Disorder is a common functional property in many proteins. Upon binding, the disordered regions can undergo coupled binding and folding, or can retain some of their disorder or "fuzziness". Two questions remain: How can disorder in a complex be beneficial? and How much disorder can occur in a biologically relevant ...

Chloroplasts are hallmark organelles of plant cells, and are the site of photosynthesis and many other essential biochemical processes. Approximately 3000 distinct proteins, representing ~95% of the total chloroplast protein complement, that support these essential processes are encoded in the nucleus and post-translationally imported into the organelle from the cytoplasm. ...

Hsp104 is a crucial thermotolerance factor in yeast that remodels protein aggregates, formed during heat stress, thus rescuing proteins that are essential for the viability of the recovering cell. One intriguing question concerns the way that Hsp104 is able to recognize and interact with a multitude of different protein substrates. ...

An emerging technique for studying protein folding and protein/protein interactions is nanopore analysis. Briefly, a biological pore is inserted into a lipid membrane. When a voltage is applied across the pore, a current will flow. However, if a large molecule passes close to the pore, called a bumping event, or ...

Elastin is the polymeric structural protein conferring the unusual properties of extensibility and elastic recoil on tissues, such as large arteries. The monomer of elastin, tropoelastin, is unusual in that glycine and proline make up more than 40% of its amino acid composition, and over 80% of its amino acids ...

Prion diseases, or transmissible spongiform encephalopathies (TSEs), are fatal neurodegenerative disorders of humans and animals caused by conformational conversion of a normal host glycoprotein (Pr[P.sup.C]) into an infectious isoform (Pr[P.sup.Sc]). A number of studies have been done to characterize the misfolding of recombinant prion protein (PrP), and the results are ...

Over the past 3 decades, many efforts have been made to identify and characterize the factors that regulate the activity of RNA polymerase II (RNAPII), the enzyme that synthesizes all the messenger RNA and many small nuclear RNAs in eukaryotes. Quite surprisingly, very little is known about the cell machinery ...

Hsp90 is a highly conserved molecular chaperone that is involved in modulating a multitude of cellular processes. Together with its cochaperone Tah1, the role of Hsp90 has been suggested in ribosomal RNA processing and the maintenance of snoRNA stability by regulating the function of an unstable protein, Pih1, in yeast ...

The rainbow smelt (Osmerus mordax) is an anadromous fish that thrives in icy seawater (-1.8[degrees]C) during winter. Smelt accumulate high levels of glycerol and moderate levels of trimethylamine oxide (TMAO), which lower the colligative freezing point of the serum and contribute to freeze resistance. Further roles of these compounds in ...

The heat shock response (Hsr) is a cellular homeostatic mechanism that is activated in response to stressful stimuli, including elevated temperatures, heavy metals, and disease states. These stresses can induce an accumulation of unfolded protein, which triggers the expression of heat shock protein (hsp) genes. Heat shock proteins (HSPs) are ...

In lipid-poor states or other conditions that result in cotranslational misfolding of apolipoprotein B100 (apoB), the defective apoB molecules are rapidly degraded by the ubiquitinproteasomal pathway, but the mechanism of delivery of apoB from the endoplasmic reticulum (ER) to the cytosolic proteasomes is not understood. By performing co-immunoprecipitations with HepG2 ...

A powerful approach for learning about the role of a specific protein in vivo would be to control that protein, through external stimuli, and monitor changes in cellular behaviour. Photocontrol of protein structure is a general approach that offers the possibility of rapid, reversible, external control of function. The azobenzene ...

In pheromone-treated yeast cells, the Ste20 PAK (p21activated kinase) is involved in transmitting the matingpheromone signal from the beta/gamma subunits of a heterotrimeric G-protein to a downstream MAP kinase cascade. A deletion of the regulatory Cdc42/Rho binding (CRIB) domain of Ste20p (Ste20deltaCRIB) modifies this protein conformation from a self-closed to ...

E-proteins are transcription factors that play critical roles in the differentiation of B-cells during lymphopoiesis. These intrinsically disordered proteins comprise an actitvation domain, ETAD1, with an LXXLL motif, which has been shown to interact with the KIX domain of the coactivator CBP/p300. A single substitution at the terminal residue in ...

Proteins are normally classified into families. Members of the families have similar overall folds, but they are different in their detailed structures. It is possible to summarize the common structural occurrence within a family. A very important feature in structures is the core set of residues, which includes most invariant ...

Ice-binding proteins include those involved in ice nucleation (INP) and antifreeze proteins (AFPs) that stop ice crystals from growing. The latter help a wide variety of organisms to either resist or better tolerate freezing. AFPs have a remarkable diversity of structures for proteins that serve the same function, and include ...

Solvation effects play a dominant role in the misfolding and aggregation of amyloidogenic peptides. Complexity of the pathways, their dependence on environmental conditions, different time and space scales--all these factors make the analysis of formation of the neurotoxic oligomers and amyloid fibrils a very challenging problem of the theoretical and ...

One of the many challenges in studies of protein folding is the delineation of folding intermediates. Intermediates are often characterized as short lived and structurally heterogeneous, making them difficult to identify by spectroscopic means. Folding pathways are frequently studied using nuclear magnetic resonance (NMR) and stopped flow fluorescence, in combination ...

Over the past decade, tremendous effort has been directed at elucidating the structure of protein folding transition states, using a protein engineering method (or Phi-value analysis). This technique uses Ala mutagenesis to probe the native structure formation surrounding a mutated side chain in the folding transition state. For Ala mutants, ...

Elastin is the extracellular matrix protein responsible for the extensibility and recoil of connective and vascular tissue. Elastic resilience is afforded, in part, by the formation of insoluble fibres, which involves the self-association of monomers through the interaction of hydrophobic domains. Contrary to the formation of highly compact amyloid-like aggregates, ...

The cytosolic chaperones Hsc70 and Hsp90 are important for the folding of proteins, as well as for the import of polypeptides into mitochondria. Cochaperones that associate in specific complexes with a mitochondrial polypeptide before import have now been analyzed. Several regulatory cochaperones of Hsc70 and Hsp90 were identified. In particular, ...

The recently designed 92-residue Top7 protein exhibits clearly non-2-state behaviors in experiments, which are markedly different from the cooperative folding of many single-domain small proteins. Using coarse-grained nativecentric chain models, including potentials with and without desolvation barriers, we predicted a stable intermediate state, in which the C-terminal fragment is folded ...

Apelin is the peptidic ligand for the membrane bound Gprotein coupled receptor APJ. A number of physiological roles for this peptide have now been identified in the cardiovascular system, in glucose metabolism, and in tumour growth. Sargent and Schwyzer hypothesized that ligands, such as apelin, are able to find and ...

Proteolipid protein (PLP) is a highly hydrophobic integral membrane protein that constitutes greater than 50% of the total protein in central nervous system myelin. Although several studies have shown that this protein exists as an oligomer in vitro, rather than as a monomer, the mechanism for this quaternary structure formation ...

Polar residues account for about 20% of residues in [alpha]-helical transmembrane (TM) regions. These residues often serve a functional role in solute transport by contributing to pore or channel formation. Polar residues may also play a structural role by promoting helix-helix interactions through side chain-side chain H-bond formation. In present ...

Water permeates all life, and mediates forces that are essential to the process of macromolecular self-assembly. Predicting these forces in a given biological context is challenging, since water organizes itself differently next to charged and hydrophobic surfaces, both of which are typically at play on the nanoscale in vivo. In ...

Antifreeze proteins (AFPs) protect cold-blooded organisms from the damage caused by freezing through their ability to inhibit ice growth. The type I AFP family, found in several fish species, contains proteins that have a high alanine content (>60% of the sequence) and structures that are almost all [alpha]-helical. We examine ...

Enteric bacteria such as Escherichia coli have acquired a wide array of acid stress response systems to counteract the extreme acidity encountered when invading the host's digestive or urinary tracts. These acid stress response systems are both enzyme and chaperone based. The 3 main enzyme-based acid resistance pathways are glutamate-, ...

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectr0ic amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary ...

Nanopore analysis can be used to study conformational changes in individual peptide or protein molecules. Under an applied voltage there is a change in the event parameters of blockade current or time when a molecule bumps into or translocates through the pore. If a molecule undergoes a conformational change upon ...